Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009429.1 Corchorus capsularis cultivar CVL-1 contig09450, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 7870
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:91 original size:2 final size:2

Alignment explanation


    Indices: 84--112  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

         74 TAAGAATCTA

                                                       
         84 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        113 ATAGGCTACA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1074 original size:30 final size:29

Alignment explanation


    Indices: 1004--1083  Score: 106
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        994 TCTCGTTTTT

                                         
       1004 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA

                *                        *
       1033 AAAAATTAAGGGGCCAATTTGTCCCAAATG
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAA-A

            * *           *      
       1063 GATAGTTAAGGGGCTAATTTG
          1 AAAAGTTAAGGGGCCAATTTG

       1084 GGTATTAAAC


Statistics
Matches: 44,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  29   27  0.61
  30   17  0.39

ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25


Consensus pattern (29 bp):   
AAAAGTTAAGGGGCCAATTTGTCCCAAAA

Found at i:3321 original size:131 final size:131

Alignment explanation


    Indices: 3095--3342  Score: 318
    Period size: 131  Copynumber: 1.9  Consensus size: 131

       3085 GTTGCCTTAA

                      *         *                 *   *             *  *     
       3095 TGATTTTGATGGTATTTTACCCAACGACTTTTTTAGTTGTTGCCAATGCTTACAATTTTTGTAAC
          1 TGATTTTGATAGTATTTTACACAACGACTTTTTTAGTTCTTGACAATGCTTACAATATTCGTAAC

                            *   *    *               *                       
       3160 AACAAAAACAAAGTCGTTGCGAAATGATAAACTATTCGTAATAACTTTATAAAAACGTTGTCTAA
         66 AACAAAAACAAAGTCGCTGCAAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGTCTAA

             
       3225 G
        131 G

                                       *                    *                
       3226 TGATTTTGATAGTATTTTACACAAC-ATTTTTTTAGTTCTTGACAATGTTTACAATATTCGTAAC
          1 TGATTTTGATAGTATTTTACACAACGACTTTTTTAGTTCTTGACAATGCTTACAATATTCGTAAC

                  *****    *                                     
       3290 AACAACTTTTTAAGTTGCTGCAAAATCATAAACTATTCGTAACAACTTTATAA
         66 AACAA-AAACAAAGTCGCTGCAAAATCATAAACTATTCGTAACAACTTTATAA

       3343 GTCGTTGTGC


Statistics
Matches: 98,  Mismatches: 18, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
 130   38  0.39
 131   60  0.61

ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39


Consensus pattern (131 bp):   
TGATTTTGATAGTATTTTACACAACGACTTTTTTAGTTCTTGACAATGCTTACAATATTCGTAAC
AACAAAAACAAAGTCGCTGCAAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGTCTAA
G

Found at i:4624 original size:47 final size:47

Alignment explanation


    Indices: 4536--4627  Score: 123
    Period size: 47  Copynumber: 2.0  Consensus size: 47

       4526 AGAAATCCTT

                                       *                   
       4536 TGACCAAAGTTGGTCTTTTCTCACTTCTATGCAAAGTTACAATTTGG
          1 TGACCAAAGTTGGTCTTTTCTCACTTCCATGCAAAGTTACAATTTGG

                  *              **          *            
       4583 TGACCACAGTTGGTCTTTTCTTGCTTCCATGC-GAGTCTACAATTT
          1 TGACCAAAGTTGGTCTTTTCTCACTTCCATGCAAAGT-TACAATTT

       4628 ATCAACCACA


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  46    3  0.08
  47   36  0.92

ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39


Consensus pattern (47 bp):   
TGACCAAAGTTGGTCTTTTCTCACTTCCATGCAAAGTTACAATTTGG

Found at i:4859 original size:61 final size:61

Alignment explanation


    Indices: 4632--4880  Score: 209
    Period size: 61  Copynumber: 4.1  Consensus size: 61

       4622 CAATTTATCA

                  *                  * *         *  *    *  *        *     
       4632 ACCACAAACTGGTCTTCTTCAA-TTCCGGACCTCAGATAGTTCTTTCTCAGTTTCAATA-TCG
          1 ACCACAGACTGGTCTTC-TCAAGTTTCAGACCTCAGACAGGTCTTCCTTAGTTT-AAAAGTCG

                             *                            *  * *   *     * 
       4693 ACCACAGACTGGTCTATTTCAA-TTCTCA-ACCTCAGACAGGTCTTTCTCAATTTCAAAGTAG
          1 ACCACAGACTGGTCT-TCTCAAGTT-TCAGACCTCAGACAGGTCTTCCTTAGTTTAAAAGTCG

                *             *       * *         *              *       
       4754 ACCATAGACTGGTCTTCTTAAGTTTCTGGCCTCAGACAAGTCTTCCTTAGTTTTAAAGTCG
          1 ACCACAGACTGGTCTTCTCAAGTTTCAGACCTCAGACAGGTCTTCCTTAGTTTAAAAGTCG

                 *                           *              *    *        
       4815 ACCACGGACTGGTCTTCTCAAGTTTCAGACCTCGGACAGGTCTTCCTTGGTTACAAAAGTCG
          1 ACCACAGACTGGTCTTCTCAAGTTTCAGACCTCAGACAGGTCTTCCTTAGTT-TAAAAGTCG

                
       4877 ACCA
          1 ACCA

       4881 GAGATTAGTC


Statistics
Matches: 151,  Mismatches: 31, Indels: 11
        0.78            0.16        0.06

Matches are distributed among these distances:
  60    8  0.05
  61  130  0.86
  62   13  0.09

ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32


Consensus pattern (61 bp):   
ACCACAGACTGGTCTTCTCAAGTTTCAGACCTCAGACAGGTCTTCCTTAGTTTAAAAGTCG
Done.